Commit 151caa0c authored by bow's avatar bow
Browse files

Add chart output of CollectRnaSeqMetrics to summary

parent 8811baae
......@@ -71,10 +71,8 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
"metrics" -> output,
"annotation" -> refFlat
) ++ Map(
"ribosomal_intervals" -> ribosomalIntervals
// TODO: this is disabled now since the file *may* not exist (e.g. when gene coverage is low)
// and it breaks the summary md5 creation
//"output_chart" -> chartOutput
"ribosomal_intervals" -> ribosomalIntervals,
"output_chart" -> chartOutput
).collect { case (key, Some(value)) => key -> value }
def summaryStats: Map[String, Any] = Picard.getMetrics(output) match {
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